The former Blue Jays ace, one of only five MLB pitchers to win the Cy Young Award as the season's top pitcher in both the American League and National League, began his 16-year career with Toronto and compiled a 203-105 record.
The eight-time All-Star won the Cy Young with Toronto in 2003 and then with the Philadelphia Phillies in 2010 to join Gaylord Perry, Pedro Martinez, Randy Johnson and Roger Clemens as a winner in both leagues.
"I was very lucky to have a lot of people in (the Toronto) organization really develop and help me become the player I was able to become," Halladay, who was traded to the Phillies ahead of the 2010 MLB season, told a news conference at MLB's Winter Meetings in Orlando.
"(I wouldn't have succeeded) without the organization's support and the people in the organization, it really turned my career around and it made a big difference in my career. At the same time, I want to reach out to the Phillies and say how much I appreciate them and everything they've done."
The 36-year-old Halladay was plagued by shoulder injuries the past two seasons with Philadelphia, making only 13 starts in 2013 with a 6.82 earned run average leading to his decision to retire.
After 12 seasons with Toronto, Halladay was keen to move on and join the Phillies, who won the 2008 World Series, to improve his chances of capturing a championship ring.
He did his part, going 21-10 with a 2.44 ERA in his first season in Philadelphia, including the 20th perfect game ever thrown, and showed his mettle in the postseason.
In his postseason debut, Halladay pitched a no-hitter in the opening game of the 2010 NL Division Series against Cincinnati, registering only the second no-hitter in MLB postseason history.
The next season, Halladay went 19-6 with a 2.35 ERA to finish second in Cy Young voting before fading due to injury.
Halladay ranks second on the Blue Jays' all-time list in wins (148), strikeouts (1,495) and shutouts (15), and rates third in ERA (3.43), starts (287), complete games (49) and innings pitched (2,046.2).
The Colorado native was Toronto's first-round selection in the 1995 MLB Draft (17th overall).
"Roy is one of the most professional and dominant pitchers of his generation and the Toronto Blue Jays are very proud and honored that he will retire as a member of our organization," Blue Jays president Paul Beeston said in a statement.